{
    "$schema": "http://json-schema.org/draft-04/schema#",
    "required": [
        "config",
        "inputs"
    ],
    "type": "object",
    "properties": {
        "inputs": {
            "required": [
                "bval",
                "bvec",
                "dwi"
            ],
            "type": "object",
            "properties": {
                "bvec": {
                    "type": "object",
                    "properties": {
                        "type": {
                            "enum": [
                                "bvec"
                            ]
                        }
                    }
                },
                "bval": {
                    "type": "object",
                    "properties": {
                        "type": {
                            "enum": [
                                "bval"
                            ]
                        }
                    }
                },
                "dwi": {
                    "type": "object",
                    "properties": {
                        "type": {
                            "enum": [
                                "nifti"
                            ]
                        }
                    }
                },
                "anatomical": {
                    "type": "object",
                    "properties": {
                        "type": {
                            "enum": [
                                "nifti"
                            ]
                        }
                    }
                }
            }
        },
        "config": {
            "required": [
                "cleanIter",
                "imresample",
                "track_algorithm",
                "computeCSD",
                "fiberWeighting",
                "life_saveOutput",
                "track_minLengthThreshMm",
                "savefigs",
                "rotateBvecsWithRx",
                "AFQ_Browser_Title",
                "life_runLife",
                "bsplineInterpFlag",
                "mrtrix_multishell",
                "track_faThresh",
                "maxDist",
                "track_whichAlgorithm",
                "mrtrix_tool",
                "life_writePDB",
                "clip2rois",
                "phaseEncodeDir",
                "ET_maxlength",
                "track_offsetJitter",
                "track_nfibers",
                "cutoffUpper",
                "cleanClippedFibers",
                "ET_numberFibers",
                "numberOfNodes",
                "track_maxLengthThreshMm",
                "AFQ_Output_Name",
                "numBootStrapSamples",
                "flipLrApFlag",
                "track_faMaskThresh",
                "life_test",
                "eddyCorrect",
                "track_wPuncture",
                "maxLen",
                "computenorms",
                "track_angleThresh",
                "track_seedVoxelOffset_1",
                "ET_angleValues",
                "life_num_iterations",
                "normalization",
                "cutoffLower",
                "ET_minlength",
                "mrtrix_mrTrixAlgo",
                "noiseCalcMethod",
                "rotateBvecsWithCanXform",
                "track_stepSizeMm",
                "nStep",
                "track_whichInterp",
                "cleanFibers",
                "ET_runET",
                "track_seedVoxelOffset_2",
                "life_discretization",
                "fitMethod",
                "dwOutMm_3",
                "dwOutMm_2",
                "dwOutMm_1"
            ],
            "type": "object",
            "properties": {
                "cleanIter": {
                    "default": 5,
                    "type": "integer"
                },
                "imresample": {
                    "default": 0,
                    "type": "integer"
                },
                "track_algorithm": {
                    "default": "mrtrix",
                    "type": "string"
                },
                "computeCSD": {
                    "default": 1,
                    "type": "integer"
                },
                "fiberWeighting": {
                    "default": 1,
                    "type": "integer"
                },
                "life_saveOutput": {
                    "default": true,
                    "type": "boolean"
                },
                "track_minLengthThreshMm": {
                    "default": 50,
                    "type": "integer"
                },
                "track_angleThresh": {
                    "default": 30,
                    "type": "integer"
                },
                "savefigs": {
                    "default": 0,
                    "type": "integer"
                },
                "rotateBvecsWithRx": {
                    "default": 0,
                    "type": "integer"
                },
                "AFQ_Browser_Title": {
                    "default": "AFQ_Browser",
                    "type": "string"
                },
                "life_runLife": {
                    "default": true,
                    "type": "boolean"
                },
                "bsplineInterpFlag": {
                    "default": 0,
                    "type": "integer"
                },
                "mrtrix_multishell": {
                    "default": false,
                    "type": "boolean"
                },
                "track_faThresh": {
                    "default": 0.2,
                    "type": "number"
                },
                "maxDist": {
                    "default": 5,
                    "type": "integer"
                },
                "mrtrix_tool": {
                    "default": "freesurfer",
                    "type": "string"
                },
                "life_writePDB": {
                    "default": false,
                    "type": "boolean"
                },
                "clip2rois": {
                    "default": 1,
                    "type": "integer"
                },
                "phaseEncodeDir": {
                    "default": 2,
                    "type": "integer"
                },
                "ET_maxlength": {
                    "default": 250,
                    "type": "number"
                },
                "track_offsetJitter": {
                    "default": 0,
                    "type": "number"
                },
                "track_nfibers": {
                    "default": 500000,
                    "type": "integer"
                },
                "cutoffUpper": {
                    "default": 90,
                    "type": "integer"
                },
                "cleanClippedFibers": {
                    "default": 0,
                    "type": "integer"
                },
                "numberOfNodes": {
                    "default": 100,
                    "type": "integer"
                },
                "cleanFibers": {
                    "default": 1,
                    "type": "integer"
                },
                "AFQ_Output_Name": {
                    "default": "afq_output",
                    "type": "string"
                },
                "numBootStrapSamples": {
                    "default": 500,
                    "type": "integer"
                },
                "flipLrApFlag": {
                    "default": 0,
                    "type": "integer"
                },
                "track_faMaskThresh": {
                    "default": 0.3,
                    "type": "number"
                },
                "life_test": {
                    "default": false,
                    "type": "boolean"
                },
                "eddyCorrect": {
                    "default": 1,
                    "type": "integer"
                },
                "track_wPuncture": {
                    "default": 0.2,
                    "type": "number"
                },
                "maxLen": {
                    "default": 4,
                    "type": "integer"
                },
                "computenorms": {
                    "default": 1,
                    "type": "integer"
                },
                "track_whichAlgorithm": {
                    "default": 1,
                    "type": "integer"
                },
                "track_seedVoxelOffset_1": {
                    "default": 0.25,
                    "type": "number"
                },
                "ET_angleValues": {
                    "default": "47.2, 23.1, 11.5, 5.7, 2.9",
                    "type": "string"
                },
                "life_num_iterations": {
                    "default": 100,
                    "type": "number"
                },
                "normalization": {
                    "default": "spm",
                    "type": "string"
                },
                "ET_numberFibers": {
                    "default": 500000,
                    "type": "number"
                },
                "ET_minlength": {
                    "default": 10,
                    "type": "number"
                },
                "mrtrix_mrTrixAlgo": {
                    "default": "iFOD2",
                    "type": "string"
                },
                "cutoffLower": {
                    "default": 10,
                    "type": "integer"
                },
                "rotateBvecsWithCanXform": {
                    "default": 1,
                    "type": "integer"
                },
                "track_stepSizeMm": {
                    "default": 1,
                    "type": "integer"
                },
                "dwOutMm_2": {
                    "default": 2,
                    "type": "number"
                },
                "track_whichInterp": {
                    "default": 1,
                    "type": "integer"
                },
                "track_maxLengthThreshMm": {
                    "default": 250,
                    "type": "integer"
                },
                "ET_runET": {
                    "default": true,
                    "type": "boolean"
                },
                "track_seedVoxelOffset_2": {
                    "default": 0.75,
                    "type": "number"
                },
                "life_discretization": {
                    "default": 360,
                    "type": "number"
                },
                "fitMethod": {
                    "default": "ls",
                    "type": "string"
                },
                "dwOutMm_3": {
                    "default": 2,
                    "type": "number"
                },
                "nStep": {
                    "default": 50,
                    "type": "integer"
                },
                "dwOutMm_1": {
                    "default": 2,
                    "type": "number"
                },
                "noiseCalcMethod": {
                    "default": "b0",
                    "type": "string"
                }
            }
        }
    },
    "title": "Invocation manifest for AFQ Pipeline: Automated Fiber Quantification Pipeline (DTIInit + MRtrix3 + ET + LiFE + AFQ)"
}